Hi
I am analyzing affymetrix data having the following experimental
design:
> analysis$design
                Normal IOP IOPC
L91RAE230 2.CEL      0   1    0
L92RAE230 2.CEL      0   1    0
L93RAE230 2.CEL      0   0    1
L94RAE230 2.CEL      0   0    1
L95RAE230 2.CEL      1   0    0
L96RAE230 2.CEL      1   0    0
 and following contrasts
> analysis$contrasts
       IOPC.IOP IOPC.Normal IOP.Normal
Normal        0          -1         -1
IOP          -1           0          1
IOPC          1           1          0
The preprocessing was done using affyPLM packge
analysis$data<-rmaPLM(analysis$raw)
where analysis$raw is AfyyBatch object. Then I fitted the the model
once with weighting matrix using AMP flags
fm<-as.matrix(analysis$Flags!="A")
analysis$fit<-lmFit(analysis$data,analysis$design,w=matrix(as.numeric(fm),dim(fm)[1],dim(fm)[2],dimnames=dimnames(fm)))
  and got a reasonable results and once without this matrix. What was
surprising is that fitting without the weighting matrix I got the
following error message:
> analysis$bayes<-eBayes(analysis$contrasts.fit)
Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
stdev.coef.lim) : 
        No residual degrees of freedom in linear model fits
I've checked the fit coeffecient matrix (analyis$fit object) and is all
NA.
Does someone have an idea why? I did not applied any weighting matrix
for this fitting.
Thanks
Ron


 

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